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- EMDB-4232: Cryo-EM reconstruction of C1-IgG1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4232
TitleCryo-EM reconstruction of C1-IgG1 complex
Map data
Sample
  • Complex: C1-IgG1 complex
    • Complex: Complement C1q
      • Protein or peptide: Complement C1q subcomponent subunit A
      • Protein or peptide: Complement C1q subcomponent subunit B
      • Protein or peptide: Complement C1q subcomponent subunit C
    • Complex: Immunoglobulin gamma-1
      • Protein or peptide: Immunoglobulin gamma-1 heavy chain
  • Ligand: water
Function / homology
Function and homology information


complement component C1 complex / complement component C1q complex / negative regulation of macrophage differentiation / synapse pruning / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer / complement activation / Classical antibody-mediated complement activation ...complement component C1 complex / complement component C1q complex / negative regulation of macrophage differentiation / synapse pruning / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer / complement activation / Classical antibody-mediated complement activation / neuron remodeling / Initial triggering of complement / immunoglobulin complex / complement activation, classical pathway / Regulation of Complement cascade / astrocyte activation / synapse organization / microglial cell activation / cell-cell signaling / amyloid-beta binding / postsynapse / collagen-containing extracellular matrix / blood microparticle / adaptive immune response / immune response / innate immune response / synapse / extracellular space / extracellular region / plasma membrane
Similarity search - Function
C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C1q subcomponent subunit A / Complement C1q subcomponent subunit B / Complement C1q subcomponent subunit C / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsUgurlar D / Howes SC / de Kreuk BJK / de Jong RN / Beurskens FJ / Koster AJ / Parren PWHI / Sharp TH / Gros P / Koning RI
CitationJournal: Science / Year: 2018
Title: Structures of C1-IgG1 provide insights into how danger pattern recognition activates complement.
Authors: Deniz Ugurlar / Stuart C Howes / Bart-Jan de Kreuk / Roman I Koning / Rob N de Jong / Frank J Beurskens / Janine Schuurman / Abraham J Koster / Thomas H Sharp / Paul W H I Parren / Piet Gros /
Abstract: Danger patterns on microbes or damaged host cells bind and activate C1, inducing innate immune responses and clearance through the complement cascade. How these patterns trigger complement initiation ...Danger patterns on microbes or damaged host cells bind and activate C1, inducing innate immune responses and clearance through the complement cascade. How these patterns trigger complement initiation remains elusive. Here, we present cryo-electron microscopy analyses of C1 bound to monoclonal antibodies in which we observed heterogeneous structures of single and clustered C1-immunoglobulin G1 (IgG1) hexamer complexes. Distinct C1q binding sites are observed on the two Fc-CH2 domains of each IgG molecule. These are consistent with known interactions and also reveal additional interactions, which are supported by functional IgG1-mutant analysis. Upon antibody binding, the C1q arms condense, inducing rearrangements of the C1rs proteases and tilting C1q's cone-shaped stalk. The data suggest that C1r may activate C1s within single, strained C1 complexes or between neighboring C1 complexes on surfaces.
History
DepositionDec 21, 2017-
Header (metadata) releaseJan 3, 2018-
Map releaseFeb 28, 2018-
UpdateOct 24, 2018-
Current statusOct 24, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.54
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.54
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6fcz
  • Surface level: 2.54
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6fcz
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4232.png

Downloads & links

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Map

FileDownload / File: emd_4232.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.274 Å
Density
Contour LevelBy AUTHOR: 2.54 / Movie #1: 2.54
Minimum - Maximum-2.3451488 - 9.467632999999999
Average (Standard dev.)0.03018134 (±0.5452338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin111
Dimensions224224224
Spacing224224224
CellA=B=C: 509.37598 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2742.2742.274
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z509.376509.376509.376
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS111
NC/NR/NS224224224
D min/max/mean-2.3459.4680.030

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Supplemental data

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Mask #1

Fileemd_4232_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_4232_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_4232_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_4232_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : C1-IgG1 complex

EntireName: C1-IgG1 complex
Components
  • Complex: C1-IgG1 complex
    • Complex: Complement C1q
      • Protein or peptide: Complement C1q subcomponent subunit A
      • Protein or peptide: Complement C1q subcomponent subunit B
      • Protein or peptide: Complement C1q subcomponent subunit C
    • Complex: Immunoglobulin gamma-1
      • Protein or peptide: Immunoglobulin gamma-1 heavy chain
  • Ligand: water

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Supramolecule #1: C1-IgG1 complex

SupramoleculeName: C1-IgG1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Complement C1q

SupramoleculeName: Complement C1q / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Immunoglobulin gamma-1

SupramoleculeName: Immunoglobulin gamma-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Complement C1q subcomponent subunit A

MacromoleculeName: Complement C1q subcomponent subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 14.914804 KDa
SequenceString:
QPRPAFSAIR RNPPMGGNVV IFDTVITNQE EPYQNHSGRF VCTVPGYYYF TFQVLSQWEI CLSIVSSSRG QVRRSLGFCD TTNKGLFQV VSGGMVLQLQ QGDQVWVEKD PKKGHIYQGS EADSVFSGFL IFPS

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Macromolecule #2: Complement C1q subcomponent subunit B

MacromoleculeName: Complement C1q subcomponent subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 14.996058 KDa
SequenceString:
TQKIAFSATR TINVPLRRDQ TIRFDHVITN MNNNYEPRSG KFTCKVPGLY YFTYHASSRG NLCVNLMRGR ERAQKVVTFC DYAYNTFQV TTGGMVLKLE QGENVFLQAT DKNSLLGMEG ANSIFSGFLL FPD

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Macromolecule #3: Complement C1q subcomponent subunit C

MacromoleculeName: Complement C1q subcomponent subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 14.302143 KDa
SequenceString:
KFQSVFTVTR QTHQPPAPNS LIRFNAVLTN PQGDYDTSTG KFTCKVPGLY YFVYHASHTA NLCVLLYRSG VKVVTFCGHT SKTNQVNSG GVLLRLQVGE EVWLAVNDYY DMVGIQGSDS VFSGFLLFPD

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Macromolecule #4: Immunoglobulin gamma-1 heavy chain

MacromoleculeName: Immunoglobulin gamma-1 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.427619 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PELLGGPSVF LFPPKPKDTL MISRTPEVTC VVVDVSHEDP EVKFNWYVDG VEVHNAKTKP REEQYNSTYR VVSVLTVLHQ DWLNGKEYK CKVSNKALPA PIEKTISKAK GQPREPQVYT LPPSRDELTK NQVSLTCLVK GFYPSDIAVE WESNGQPENN Y KTTPPVLD ...String:
PELLGGPSVF LFPPKPKDTL MISRTPEVTC VVVDVSHEDP EVKFNWYVDG VEVHNAKTKP REEQYNSTYR VVSVLTVLHQ DWLNGKEYK CKVSNKALPA PIEKTISKAK GQPREPQVYT LPPSRDELTK NQVSLTCLVK GFYPSDIAVE WESNGQPENN Y KTTPPVLD SDGSFFLYSK LTVDKSRWQQ GNVFSCSVMH EALHNHYTQK SLSLSPGK

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 198 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79120
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6fcz:
Model of gC1q-Fc complex based on 7A EM map

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